Compositions and methods for clonal amplification and analysis of polynucleotides

ABSTRACT

Compositions and methods of use are disclosed for clonally amplifying and analyzing one or more polynucleotides.

1. CROSS REFERENCE TO RELATED APPLICATIONS

This application claims benefit under 35 U.S.C. § 119(e) to applicationSer. No. 60/662,961 filed Mar. 16, 2005, the contents of which areincorporated herein by reference.

2. BACKGROUND

Current methods for routine and large scale analysis of targetpolynucleotides require the preparation of tens to thousands to millionsof individual target samples, which are processed and analyzed inindividual reaction vessels. Therefore, labor, materials, and equipmentmake up a significant cost of any target polynucleotide analysisregardless of the methodology employed.

To increase the number of target polynucleotides that can be discretelyand simultaneously analyzed, the present disclosure includescompositions and methods for clonally amplifying target polynucleotidesequences and the parallel analysis of the amplified sequences.

3. SUMMARY

These and other features of the present teachings are set forth herein.

This disclosure provides compositions, methods, and kits for theanalysis of polynucleotides. In general, the disclosure provides methodsof isolating and clonally amplifying polynucleotides to produce isolatedpopulations of amplicons (“clonal amplicons”). In some embodiments, verylarge numbers of polynucleotides can be isolated and clonally amplifiedin parallel.

Polynucleotides can be isolated and clonally amplified by variousmethods. In some embodiments, polynucleotides can be isolated andclonally amplified by insertion into recombinant vectors, which can beintroduced into a host cell suitable for replicating the vector.Polynucleotides also can be isolated and clonally amplified and placedin a reaction vessel or in a hydrophilic compartment of an inverseemulsion.

Various methods or techniques can be used to clonally amplify isolatedpolynucleotides, such as, PCR, including exponential, linear,log-linear, and asymmetric PCR. Therefore, in some embodiments, clonalamplification reactions can include one or more primers. In someembodiments, a primer used in a clonal amplification reaction can beattached to a surface, such as, a microparticle, bead or a slide. Insome embodiments, a surface can comprise a plurality of primers.Therefore, in various exemplary embodiments, the products of clonalamplification (i.e., isolated populations of clonal amplicons) can beattached to a surface.

In some embodiments, a primer attached to a surface can be used toclonally amplify a polynucleotide isolated in a hydrophilic compartmentof an inverse emulsion. In some embodiments, (e.g., when a primer isattached to a microparticle) the entire surface of the microparticle canbe completely contained within the hydrophilic compartment. In someembodiments, (e.g., when a primer is attached to a slide) thehydrophilic compartment can be disposed upon the slide, and therefore,may not be completely contained within the hydrophilic compartment. Insome embodiments, a surface to which a primer is a attached can beexternal to the hydrophilic compartment.

In some embodiments, polynucleotides can be selected for analysis to theexclusion of other polynucleotides or polynucleotide sequences that canbe present in sample. For example, in some embodiments, polynucleotidescan be selected based on their suitability for incorporation into arecombinant vector and/or their suitability for replication by varioushost cells.

In some embodiments, polynucleotides can be selected using a multiplexamplification reaction. In some embodiments, a multiplex amplificationreaction is suitable to select and amplify hundreds, thousands, hundredsof thousands, or millions of polynucleotides to produce multiplexamplicons, that can be isolated and clonally amplified.

Once made, the clonal amplicons can be analyzed by various methods. Insome embodiments, the methods of analysis can be suitable for analyzingvarious populations of isolated clonal amplicons in parallel. The numberof clonal amplicons that can be analyzed in parallel can be determinedat the discretion of the practitioner and can include hundreds,thousands, hundreds of thousands, or millions of clonal amplicons. Themethods of analysis include but are not limited to detection, singlenucleotide polymorphism analysis, sequencing and the like. In variousexemplary embodiments, sequencing can be by parallel sequencing,pyrosequencing, fluorescence in situ sequencing, or massively parallelsignature sequencing.

4. BRIEF DESCRIPTION OF THE FIGURES

The skilled artisan will understand that the drawings, described below,are for illustration purposes only. The drawings are not intended tolimit the scope of the present teachings in any way.

FIG. 1 illustrates an embodiment of multiplex amplification of atranscriptome 1 by polymerase chain reaction (PCR). Each forward 10 andreverse primer 20 pair contains a forward 30 and reverse 40 universalsequences that are incorporated into each amplicon 50.

FIG. 2 illustrates an embodiment of an inverse emulsion 120 comprising ahydrophobic phase 125 and a plurality of hydrophilic compartments130A-D. Hydrophilic compartment 130A contains isolated polynucleotide200, multiple copies of reverse primer 80, and multiple copies offorward primer 100 attached to microparticle 90. Clonal amplification ofpolynucleotide 200 by PCR yields an isolated population of doublestranded clonal amplicons 105 attached to microparticle 90.

FIG. 3 illustrates an embodiments of an inverse emulsion 150 comprisinga plurality of hydrophilic compartments 140A-B disposed upon surface110. Compartment 140A contains isolated target polynucleotide 60,multiple copies of reverse primer 80, and multiple copies of forwardprimer 100 attached to surface 110.

FIG. 4 illustrates an embodiment of clonal amplicons 200, 300, 400attached to discrete areas of a surface 110.

5. DETAILED DESCRIPTION

It is to be understood that both the foregoing general description,including the drawings, and the following detailed description areexemplary and explanatory only and are not restrictive of thisdisclosure. In this disclosure, the use of the singular includes theplural unless specifically stated otherwise. Also, the use of “or” means“and/or” unless stated otherwise. Similarly, “comprise,” “comprises,”“comprising” “include,” “includes,” and “including” are not intended tobe limiting.

This disclosure provides compositions, methods, and kits for theanalysis of polynucleotides. In general, the disclosure provides methodsof isolating and amplifying polynucleotides under conditions suitablefor producing isolated populations of amplified sequences. “Isolated” asused herein refers to placed or standing alone, discrete, detached,separated from others. Therefore, “isolated polynucleotide” as usedherein refers to a polynucleotide that is detached or separated fromother polynucleotides in a manner and under conditions suitable to yieldisolated groups or populations of amplified sequences (“amplicons”). Theamplicons that comprise any given isolated population can be traceddirectly or indirectly to an isolated polynucleotide and can be referredto as “amplicon clones” or “clonal amplicons”. Therefore, the disclosedmethods of isolating and amplifying polynucleotides to yield isolatedpopulations of amplicons can be referred to as “clonal amplification”.The methods and techniques employed in the analysis of clonal ampliconscan be selected at the discretion of the practitioner and include butare not limited to detection, sequencing, resequencing, quantitation,single-nucleotide polymorphism analysis, and the like.

The methods disclosed herein are suitable for analyzing complexpolynucleotides and complex mixtures of polynucleotides. For example, insome embodiments, the disclosed methods can be used to sequence anentire genome of a cell, organism, or virus. However, in someembodiments, the methods disclosed herein can be used to select a subsetof specific polynucleotides sequences of a genome for analysis.Therefore, in some embodiments, specific polynucleotide sequences ofinterest can be selected, clonally amplified, and analyzed to theexclusion of other polynucleotide sequences that may be present in asample. As described in more detail below, various methods andtechniques can be used to select polynucleotides of interest. Theseinclude but are not limited to amplification techniques (e.g., PCRtechniques), hybridization techniques insertion of polynucleotides ofinterest into a recombinant vector, and the like. The methods disclosedherein are suitable for clonal amplification and analysis of a pluralityof polynucleotides. In some embodiments, a plurality of polynucleotidescan be clonally amplified and analyzed in parallel. “Parallel reaction”as used herein refers to a reaction solution comprising a plurality ofdiscrete regions suitable for performing a plurality of reactionsconcurrently. In some embodiments, the discrete regions of a parallelreaction can be in fluidic communication. Therefore, in someembodiments, reactants and/or products can be exchanged between thevarious discrete regions. However, in general, certain reactants,including but not limited to, polynucleotides and clonal amplicons areretained within discrete regions of a parallel reaction to facilitatetheir analysis by the methods disclosed herein. Virtually any number ofpolynucleotides can be clonally amplified and analyzed. For example, invarious exemplary embodiments, hundreds, thousands, hundreds ofthousands millions, and even greater numbers of polynucleotides can beanalyzed in parallel by the disclosed methods. In various exemplaryembodiments the numbers of polynucleotides analyzed in parallel can beat least 100, 500, 1000, 10000, 50000, 100000, 300000, 500000, or1000000.

In some embodiments, limiting dilution can be used to isolatepolynucleotides in a manner that is suitable for clonal amplification.For example, a sample comprising a plurality of polynucleotides can bediluted to a concentration such that aliquots of the diluted sample thatcan be placed into individual reaction vessels (e.g., wells of amulti-well plate) can be predicted to comprise on average >0 and <1polynucleotide. Therefore, a percentage of reaction vessels can bepredicted on a statistical basis (e.g., Poisson distribution) tocomprise an isolated polynucleotide suitable for clonal amplification.Determining a dilution suitable for obtaining isolated polynucleotidesis within the abilities of the skilled artisan. Factors to be consideredinclude but are not limited to the polynucleotide concentration and theexpected number, types, and composition of various polynucleotides thatmay be present in a sample. In some embodiments, a dilution suitable forobtaining isolated polynucleotides from a sample can be determinedempirically. Once isolated within the reaction vessels, polynucleotidescan be amplified by various methods as described below to produce clonalamplicons.

In some embodiments, a semi-solid or gel matrix can be used to isolatepolynucleotides in a manner suitable for clonal amplification. In someembodiments, this can be accomplished by mixing polynucleotides at asuitable concentration with a matrix-forming material and allowing thematerial to set (e.g., agarose, acrylamide, etc.) The composition andconsistency of the matrix can be selected at the discretion of thepractitioner. However, in some embodiments, the matrix can be suitablefor retaining polynucleotides and amplified sequences at discretelocations within the matrix while allowing diffusion of one or morereagents used for amplification or analysis (e.g, dNTPs, ddNTPs, enzymecofactors (e.g., Mg²⁺, Mn²⁺), buffers, ions). The skilled artisan willappreciate that one or more reagents used for amplification or analysismay not be suitable for diffusion within a matrix (e.g. primers, probes,enzymes (e.g., thermostable polymerase)). Therefore, such reagents canbe added to the matrix-forming material before the matrix forms.Therefore, in some embodiments, polynucleotides suitable for clonalamplification and analysis can be diluted, as needed, and combined witha matrix-forming material and one or more reagents required foramplification or analysis. A matrix comprising isolated polynucleotidescan be allowed to form on a solid support (e.g., a glass slide).However, the skilled artisan will appreciate that other types ofsupports having various shapes and dimensions also can be utilized. Onceisolated with a matrix, a polynucleotide can be amplified by variousmethods as described below to produce isolated populations of clonalamplicons within the matrix. In some embodiments, polynucleotidesisolated within a matrix can be amplified by placing the matrix in asolution comprising an appropriate buffer, pH, and other components thatcan diffuse into the matrix (e.g., dNTPs, enzyme co-factors, ions (Na⁺,Cl⁻, Mg²⁺)) to provide or maintain suitable amplification conditions.

In some embodiments, polynucleotides suitable for clonal amplificationcan be isolated by hybridization to a probe attached to a solid support.For example, a solid support (e.g., a glass slide) can comprise aplurality of regions, wherein each region comprises probes suitable forspecifically hybridizing to a polynucleotide of interest. Therefore, apolynucleotide of interest can be isolated within each region bycontacting the support with a sample under conditions suitable forspecific hybridization. In some embodiments, a probe hybridized to apolynucleotide of interest also can function as a primer and, therefore,can be extended by a polymerase to produce a sequence complementary to apolynucleotide of interest. In some embodiments, the polynucleotide ofinterest can be disassociated from the extended probe and the processcan be repeated. As a result, single-stranded clonal amplicons attachedto a solid support can be produced. In some embodiments, a primer can behybridized to a single-stranded clonal amplicon to produce additionalcopies of the polynucleotide of interest. These additional copies can behybridized to other probes and provide a template for probe extension.The skilled artisan will appreciate that in some embodiments if asuitable amount of primer is present each of the single-stranded clonalamplicons can be made to be double stranded.

In some embodiments, polynucleotides suitable for clonal amplificationcan be isolated using recombinant DNA techniques that are well-known inthe art. (Sambrook et al., Molecular Cloning: A Laboratory Manual (3d.ed. Cold Spring Harbor Laboratory Press)) For example, in someembodiments, individual polynucleotides can be inserted into recombinantvectors which can be introduced into host cells capable of replicatingthe vector. The reaction conditions under which polynucleotides areintroduced into recombinant vectors can be designed to favor theinsertion of a single polynucleotide into each vector. In someembodiments, this can be accomplished by utilizing a concentration ofvector that is in molar excess (e.g., ≧10X) of the polynucleotides.Similarly, to favor the transformation of a single host cell by a singlevector, host cells can be utilized at a concentration in molar excess ofthe vectors. In some embodiments, a recombinant vector can be designedto favor the insertion of polynucleotides of interest over otherpolynucleotides that may be present in a sample. As the skilled artisanwill appreciate this can be accomplished by various methods known in theart. For example, in some embodiments, a vector can comprise 5′-singlestranded sequences or “sticky-ends” to favor the insertion ofpolynucleotides having 5′-sequences complementary to the sticky-ends ofthe vector. As the skilled artisan also will appreciate, various typesof selection techniques (e.g., antibiotic susceptibility, metabolicproperties (e.g., lactose utilization)) can be utilized to identify andisolate host cells comprising vectors having an inserted polynucleotide.Determining the type of vectors suitable for use with variousprokaryotic and eukaryotic host cells is within the abilities of theskilled artisan. Once the recombinant vector comprising an insertedpolynucleotide is introduced into an appropriate host cell, the vectorand the inserted polynucleotide are clonally amplified by the host celland then harvested for analysis.

In some embodiments, polynucleotide sequences suitable for clonalamplification can be isolated within a hydrophilic compartment of aninverse emulsion. (U.S. Pat. Nos. 5,616,478, 5,958,698, 6,001,568,6,432,360, 6,485,944, 6,511,803, 6,440,706, 6,753,147, 6,753,147, U.S.Application Serial Nos. 2002090629, 2002120126, 2002120127, 2002127552,2003124594; WO0109386; WO0109386; Dressman et al., 2003, Proc. Natl.Acad. Sci. USA 100(15):8817-22; Mitra et al., 1999, Nucleic Acids Res.27(24):e34; and Shendure et al., 2004, Nat. Rev. Genet. 5(5):335-44,incorporated by reference). “Inverse emulsion”, “water-in-oil emulsion”(“W/O”) and grammatical equivalents as used herein refer to a colloidalcomposition comprising a discontinuous hydrophilic phase distributed asdiscrete compartments in a continuous, hydrophobic phase. In variousexemplary embodiments, the hydrophilic phase compartments can comprise asemi-solid or matrix material (e.g., agarose, acrylamide) or cancomprise an aqueous solution (“aqueous droplet”). As the skilled artisanwill appreciate, the dimensions of the hydrophilic compartments ingeneral are not uniform and their average dimensions can be dependentupon several factors, including but not limited to the composition ofthe hydrophobic and hydrophilic phases and the method used to preparethe emulsion. In various exemplary embodiments, the mean diameter ofhydrophilic compartments can be about 0.5 μm, 1 μm, 2 μm, 3 μm, 4 μm, 5μm, 6 μm, 7 μm, 8 μm, 9 μm, 10 μm, 20 μm, 30 μm, 40 μm, 50 μm, 60 μm, 70μm, 80 μm, 90 μm, 100 μm, 150 μm, 200 μm, 250 μm, 300 μm, 350 μm, 400μm, 450 μm to about 500 μm. In various exemplary embodiments, the meanvolume of hydrophlic compartments can be about 0.5 μm³ to about4,000,000 μm³, from about 500 μm³ to about 500,000 μm³, from about 8,000μm³ to about 200,000 μm³. However, larger and smaller compartments alsocan be contemplated. Non-limiting examples of factors that can beconsidered in determining a suitable volume or diameter of a hydrophiliccompartment include but are not limited to the clonal amplificationconditions, the method of analyzing the clonal amplicons, and the “spotsize” of the hydrophilic compartment, as described below.

The composition of the continuous and discontinuous phases of an inverseemulsion can be selected at the discretion of the practitioner. Invarious exemplary embodiments a continuous phase can be can include anoil (e.g., mineral oil, light mineral oil, silicon oil) or a hydrocarbon(e.g., hexane, heptane, octane, nonane, decane, etc.) and the like. Thecomposition of the various phases can be selected to provide a suitableemulsion under the conditions of clonal amplification. Therefore,“suitable emulsion” and equivalents refer to an emulsion that does notsubstantially degrade, collapse or in which the hydrophilic compartmentsdo not substantially coalesce under the clonal amplification conditions.Therefore, in various exemplary embodiments, an emulsion can be suitablefor carrying out reactions at varying temperatures (e.g., thermocycling,such as, PCR), and other conditions (e.g., pH, ionic strength,hybridization conditions, etc.), and in the presence of various reactioncomponents (e.g., nucleic acids, proteins, enzymes, catalysts,co-factors, intermediates, products, by-products, labels,microparticles, etc.).

In some embodiments an inverse emulsion can comprise compositions orcompounds that modify the inverse emulsion's stability. In someembodiments, such compounds can be amphipathic and therefore comprisehydrophobic and hydrophilic groups. In various exemplary embodiments,the hydrophilic group can be polar, positively charged or negativelycharged. The skilled artisan can appreciate that amphipathic compounds,depending on their concentration and the composition of the variousphases, can be used to increase or decrease the stability of an inverseemulsion. Examples of amphipathic compounds include but are not limitedto proteins, polypeptides, and surfactants, such as, detergents andemulsifiers, all of which can be used alone or in any combination. Forexample, an amphipathic compound can be a protein or polypeptide (e.g.,albumin), lecithin, sodium oleate, glycolic acid ethoxylate oleyl ether,4-(1-aminoethyl)phenol propoxylate, glycolic acid ethoxylate4-tert-butylphenyl ether, glycolic acid ethoxylate oleyl ether, sodiumdodecyl sulfate,3-[(3-cholamidopropyl)dimethylammonia]-1-propanesulfonate,n-dodecyl-β-D-maltoside (lauryl-β-D-maltoside),n-octyl-β-D-glucopyranoside, n-octyl-β-D-thioglucopyranoside (OTG),4-(1,1,3,3-tetramethylbutyl)phenol polymer, N-lauroylsarcosine,polyethylene-block-poly(ethylene glycol), sodium7-ethyl-2-methyl-4-undecyl sulfate, glycolic acid ethoxylate laurylether, Altox® 4912, Tween® 20, Tween® 80, sorbitan monooleate (Span 80),Triton® X-100, Triton® X-114, Brij®-35, Brij®-58,3-[(3-cholamidopropyl)-dimethylammonio]-1-propane-sulfonate (CHAPS),Nonidet P-40 (NP-40). For further description of these and/or otheramphipathic compounds and methods of use in emulsions see, e.g., Becher,Emulsions: Theory and Practice, 3rd ed. Oxford University Press 2001(ISBN 0841234965); Becher (ed.) Encyclopedia of Emulsion Technology:Basic Theory Vol. I-IV, Marcel Dekker Inc. 1983 (ISBN: 0824718763), 1985(ISBN: 0824718771), 1987 (ISBN: 082471878X), 1996 (ISBN: 0824793803);Holmberg, Surfactants and Polymers in Aqueous Solutions 2nd ed., JohnWiley & Sons 2002 (ISBN: 0471498831); Lissant (ed.), Emulsions andEmulsion Technology. Marcel Dekker Inc. 1984 (ISBN: 0824770838);Lissant, Emulsions and Emulsion Technology (Surfactant Science). MarcelDekker Inc. 1974 (ISBN: 0824760972); Lissant (ed.), Emulsions andEmulsion Technology/Part II (Surfactant Science, Vol. 6). Marcel DekkerInc. 1974 (ISBN 0824718925); Lissant, Emulsions and Emulsion TechnologyMarcel Dekker Inc. 1984 (ISBN: 0824790472); Handbook of IndustrialSurfactants (ISBN 1890595209).

Methods of making inverse emulsions are known in the art and include butare not limited drop wise addtion of an aqueous solution into a stirredhydrophobic solution optionally comprising one or more amphipathiccompounds (see, e.g., Becher, Emulsions: Theory and Practice, 3rd ed.Oxford University Press 2001 (ISBN 0841234965); Becher (ed.)Encyclopedia of Emulsion Technology: Basic Theory Vol. I-IV, MarcelDekker Inc. 1983 (ISBN: 0824718763), 1985 (ISBN: 0824718771), 1987(ISBN: 082471878X), 1996 (ISBN: 0824793803); Dressman et al., 2003,Proc. Natl. Acad. Sci. USA. 100(15):8817-22 (Epub 2003 Jul. 11);Ghadessey et al., 2001, Proc. Natl. Acad. Sci. USA. 98:4552-7; Griffithset al., 2003, EMBO 22:24-35; Lissant (ed.), Emulsions and EmulsionTechnology. Marcel Dekker Inc. 1984 (ISBN: 0824770838); Lissant,Emulsions and Emulsion Technology (Surfactant Science). Marcel DekkerInc. 1974 (ISBN: 0824760972); Lissant (ed.), Emulsions and EmulsionTechnology/Part II (Surfactant Science, Vol. 6). Marcel Dekker Inc. 1974(ISBN 0824718925); Lissant, Emulsions and Emulsion Technology MarcelDekker Inc. 1984 (ISBN: 0824790472); Nakano et al., 2003, J. Biotechnol.102(2):117-24; Tawfik et al., 1998, Nat. Biotechnol. 16(7):652-6; U.S.Pat. No. 6,489,103; and WO 2002/22869). Therefore, in some embodiments,polynucleotides and reagents suitable for clonal amplification oranalysis can be isolated within hydrophilic compartments by drop-wiseaddition of an aqueous solution comprising the polynucleotides and suchreagents into a stirred hydrophobic solution. In some embodiments, thepolynucleotide concentration of the aqueous solution can be adjustedsuch that hydrophilic compartments of the inverse emulsion averagefrom >0 to <1 polynucleotide per compartment.

In some embodiments, emulsion formation can be monitored byhigh-resolution ultrasonic spectroscopy in which changes in ultrasonicvelocity and attenuation that occur as a function of time are indicativeof emulsion formation, as known in the art. In some embodiments, thesize (e.g., mean droplet diameter), number, and/or composition of thehydrophilic compartments can be analyzed to sort or remove hydrophiliccompartments unsuitable for clonal amplification or analysis. Therefore,in some embodiments, probes (e.g., molecular beacons), primers (e.g.,scorpions), labels (fluorescent molecules) and other moieties (e.g.,magnetic beads) can be included in the hydrophilic compartments toprovide a detectable signal or moiety that can be used to identifyhydrophilic compartments of interest. Therefore, methods suitable forsorting hydrophilic compartments include but are not limited tomicroscopic examination (Vogelstein et al., 1999, Proc. Natl. Acad. Sci.USA 96:9236-9241; Dressman et al., 2003, Proc. Natl. Acad. Sci. USA.100(15):8817-22 (Epub 2003 Jul. 11) or laser diffraction (Tawfik et al.,1998, Nat. Biotechnol. 16(7):652-6), laser Dopplervelocimetry/anemometry (“LDV” or “LDA”), flow cytometry, microflowcytometry, affinity chromatography (e.g., columns and/or pads), exposureto magnetic fields, and the like.

In some embodiments, the aqueous solution comprising the polynucleotidesthat can be used to form an inverse emulsion also can comprise all ofthe reagents suitable for clonal amplification. Therefore, in someembodiments, when the inverse emulsion is formed it can be incubatedunder conditions suitable to clonally amplify the polynucleotidesisolated within the various compartments. In some embodiments, one ormore clonal amplification reagents can be omitted from the aqueoussolution comprising the polynucleotides used to form the inverseemulsion. Therefore, in some embodiments, these and other reagents, suchas reagents suitable for detection or analysis of the clonal amplicons,can be introduced into the hydrophilic compartments after the inverseemulsion is formed as described below.

Once the polynucleotides are isolated they can be clonally amplifiedusing the principals and techniques of various methods known in the art.Selecting a method suitable for clonal amplification of isolatedpolynucleotides is within the abilities of the skilled artisan. Methodssuitable for clonal amplification include but are not limited to PCR(see, e.g., U.S. Pat. Nos. 4,683,195, 4,683,202, 4,800,159, 4,965,188,5,075,216, 5,176,995, 5,338,671, 5,386,022, 5,333,675, 5,340,728,5,405,774, 5,436,149, 5,512,462, 5,618,703, 5,656,493, 6,037,129,6,040,166, 6,197,563, 6,300,073, 6,406,891, 6,514,736; EP-A-0200362,EP-A-0201184, U.S. Application Ser. No. 60/584,665, Edwards et al.(eds.), 2004, Real-Time PCR: An Essential Guide. Horizon BioscienceNorfolk, UK (ISBN 0-9545232-7-X)), LCR (see, e.g., EP-A-320308 and U.S.Pat. Nos. 5,427,930, 5,516,663, 5686272, and 5869252), OLA (see, e.g.U.S. Pat. Nos. 4,883,750, 5,242,794, 5521065, 5962223; Brinson et al.,1997, Genet. Test. 1(1):61-8. Erratum in: Iovannisci, 1998, Genet. Test.2(4):385; Grossman et al., 1994, Nucleic Acids Res. 22(21):4527-34.Erratum in: Iovannisci, 1998, Nucleic Acids Res. 26(23):5539; lannone etal., 2000, Cytometry 39(2):131-40; Nickerson et al., 1990, Proc. Natl.Acad. Sci. USA. 87(22):8923-7), Q-beta amplification (see, e.g. U.S.Pat. Nos. 4,786,600, 4,9578, 585,356,774, 5,364,760, 5,503,979,5,602,001, 5620851; “Amplifying Probe Assays with Q-Beta Replicase”Bio/Technology 1989: 7(6), 609-10 (Eng.); Pritchard, 1990, J. Clin. Lab.Anal. 4:318), NASBA™ (Burchill et al., 2002, Br. J. Cancer. 86(1):102-9;Deiman et al., 2002, Mol. Biotechnol. 20(2):163-79; Malek et al.“Nucleic Acid Sequence-Based Amplification (NASBA™)” Ch. 36 In Methodsin Molecular Biology, Vol. 28: Protocols for Nucleic Acid Analysis byNonradioactive Probes, Isaac (ed.) Humana Press, Inc., Totowa, N.J.(1994); Romano et al., 1997, Immunol. Invest. 26(1-2):15-28), stranddisplacement amplification ((SDA) U.S. Pat. Nos. 5,270,184 and5,455,166; Walker. “Empirical Aspects of Strand DisplacementAmplification” In PCR Methods and Applications, 3(1):1-6 Cold SpringHarbor Laboratory Press, Cold Spring Harbor, N.Y. (1993), rolling circleamplification (RCA), transcription, and reverse transcription.

In some embodiments, isolated polynucleotides can be clonally amplifiedusing a primer attached to a solid support or surface (e.g., a chip,slide, membrane, gel). Therefore, in some embodiments, clonalamplification reactions can yield a surface comprising a plurality ofisolated clonal amplicons. In various exemplary embodiments, a solidsupport may have a wide variety of forms, including membranes, slides,plates, micromachined chips, microparticles, beads and the like. Solidsupports may comprise a wide variety of compositions including, but notlimited to, glass, plastic, silicon, alkanethiolate derivatized gold,cellulose, low cross linked and high cross linked polystyrene, silicagel, polyamide, and the like, and can have various shapes and features(e.g., wells, indentations, channels, etc.). Methods of attachingprimers to a surface are known in the art (see, e.g., Beier et al.,1999, Nucleic Acids Res. 27(9):1970-1977; Brison et al., 1982, Molecularand Cellular Biology 2:578 587; Cheung et al., 1999, Nat. Genet 21(1Suppl):15-19; Chrisey et al., 1996, Nucleic Acids Res. 24(15):3031-3039;Cohen et. al., 1997, Nucleic Acids Res. 1997 Feb. 15; 25(4):911-912;Devivar et al., 1999, Bioorg. Med. Chem. Lett. 9(9):1239-1242; Heme etal., 1997. J. Am. Chem. Soc. 119:8916-8920; Kumar et al., 2000, NucleicAcis Res. 28(14):e71; Lipshutz et al., 1999, Nat. Genet. 21(1Suppl):20-24; Milner et al., 1997, Nat. Biotechnol. June;15(6):537-541;Morozov et al., 1999, Anal. Chem. 71(15):3110-3117; Proudnikov et al.,1998, Anal Biochem. 259(1):34-41; Rasmussen et al., 1991, Anal Biochem.198(1):138-142; Rogers et al., 1999, Anal. Biochem. 266(1):23-30; Saloet al., 1999, Bioconjug Chem. 10(5):815-823; Singh-Gasson et al., 1999,Nat. Biotechnol. 17(10):974-978, and Pierce Chemical Company Catalog1994, pp. 155-200), incorporated herein by reference).

A non-limiting example of the use of a primer attached to amicroparticle to clonally amplify a polynucleotide in a hydrophiliccompartment of an inverse emulsion is illustrated in FIG. 2. In FIG. 2,are shown inverse emulsion 120 comprising hydrophobic phase 125 and aplurality of hydrophilic compartments 130A-D. Hydrophilic compartment130A contains isolated polynucleotide 200, multiple copies of reverseprimer 80, and multiple copies of forward primer 100 attached tomicroparticle 90. Therefore, FIG. 2 illustrates an embodiment whereinthe entire surface to which a primer is attached is completelycontained, confined, or encased within a hydrophilic compartment. Clonalamplification of polynucleotide 200 by PCR will yield an isolatedpopulation of double stranded clonal amplicons 105 attached tomicroparticle 90.

To analyze double stranded clonal amplicons attached to microparticles,the emulsion can be collapsed and the microparticles can be collected.Methods of collapsing an inverse emulsion are known in the art andinclude but are not limited to modifying the concentration of anamphipathic compound in the emulsion and centrifugation. In someembodiments, the double stranded clonal amplicons can be denatured,leaving one strand of the clonal amplicons attached to themicroparticles. In some embodiments, the microparticles can bedistributed into wells of a multi-well plate and analyzed as disclosedherein.

A non-limiting example of the use of primers attached to a surface toclonally amplify a polynucleotide in a hydrophilic compartment of aninverse emulsion is illustrated in FIG. 3. In FIG. 3, are shown inverseemulsion 150 comprising a plurality of hydrophilic compartments 140A-Bdisposed upon surface 110. Compartment 140A contains isolated targetpolynucleotide 60, multiple copies of reverse primer 80, and multiplecopies of forward primer 100 attached to surface 110. Therefore, FIG. 3illustrates an embodiment wherein a hydrophilic compartment is disposedupon the surface to which a primer is attached. Although, FIG. 3illustrates an embodiment in which a primer can be attached to asurface, other reagents suitable for amplification and analysis also canbe attached to the surface at the discretion of the practitioner. Insome embodiments, a surface can contain a coating of film of lyophilizedor partially lyophilized reagents which can become reconstituted whencontacted with a hydrophilic compartment. Clonal amplification ofpolynucleotide 60 will yield an isolated population of double strandedclonal amplicons attached to surface 100 that are restricted to the areacorresponding to the “spot-size” of hydrophilic compartment 140A. Thisis further shown in FIG. 4, which illustrates an embodiment in which aplurality of isolated populations of clonal amplicons 200, 300, 400 canbe attached to discrete locations of surface 110.

In some embodiments, a primer can be attached to a surface and canproject into an aqueous compartment without the aqueous compartmentcontacting the surface. Therefore, in some embodiments the surface canbe external to the aqueous compartment. In some embodiments,electrostatic forces from for example an attachment moiety or linker,and/or the surface can prevent an aqueous compartment from contactingthe surface.

In some embodiments, polynucleotides that can be isolated, clonallyamplified, and analyzed by the disclosed methods can be specific regionsof a complex polynucleotide (e.g., a chromosome) or selected fromcomplex mixtures of polynucleotides (e.g., a genome; nucleic acidlibraries, etc.). Thus, various aspects or characteristics of complexpolynucleotides, such as a genome or a cell or organism, can bespecifically targeted and analyzed. Non-limiting examples of genomicregions that can be specifically targeted include but are not limited tocis-acting regulatory elements, regions of rearrangement (e.g., antibodyand T-cell receptor genes, oncogenes), recombination, insertion (e.g.viral insertion, e.g., retroviral insertion), deletion, geneduplication, transpositional elements, highly-repetitive sequences,specific genes (e.g., genes that encode RNA or protein (e.g., cell cycleregulators, transcription factors, replication/repair proteins, etc.),pseudogenes, transcribed genes (e.g., the transcriptome), genomicregions associated with a disease state (e.g., cancer, cognitivedisorders, birth defects, drug addiction, psychiatric disorders,autoimmune disease etc.) can be selectively analyzed by the disclosedmethods. In some embodiments, specific regions of a genome can beselected and analyzed at any one or more stages of a cell cycle, ordifferentiation, or in response to natural (e.g., antigens, cytokines,hormones, etc.) and/or artificial stimuli (e.g., carcinogens, mutagens,pharmaceuticals etc.). Thus, in some embodiments, the methods disclosedherein can be used to selectively determine the expression and/ortranscription profile of one or more cells by selectively targetinggenomic regions of interest. In various exemplary embodiments, about 1,5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 76, 80, 85, 90,95 or about 100% of a genome can be analyzed by the disclosed methods.

In some embodiments, polynucleotides can be selected for clonalamplification by multiplex amplification of polynucleotide sequences.Therefore, in some embodiments, the disclosed methods can comprisemultiplex amplification of polynucleotide sequences to produce aheterogeneous mixture of amplicons (“non-clonal amplicons” or “multiplexamplicons”). Once made, the multiplex amplicons can be isolated,clonally amplified, and analyzed.

In various exemplary embodiments, multiplex amplicons can be made by PCRamplification, which can include exponential, linear, asymmetric, and/orlog-linear PCR (see, e.g., U.S. Application Ser. No. 60/584,665). Insome embodiments, multiplex PCR amplification conditions can be designedto reach a plateau. “Plateau” herein refers to the stage of anamplification reaction (e.g., PCR) when synthesis and consequentaccumulation of amplicons may terminate even though primers, template,polymerase and dNTPs can be present. This can occur when hybridizationof the first and second strands of double-stranded amplicons to eachother competes with the hybridization of the amplification primers tothe individual amplicon strands. In some embodiments, a plateau canoccur when one or more reagents are consumed (see, e.g., Saunders,Quantitative Real-Time PCR 106, 108 (Edwards et al. eds., 2004 (HorizonBioscience, Norfolk UK, ISBN 0-9545232-7-X)); and Bustin et al.,Analysis of mRNA Expression by Real-Time PCR 127 (Edwards et al. eds.,2004 (Horizon Bioscience, Norfolk UK, ISBN 0-9545232-7-X))). However, insome embodiments, amplification conditions can be designed to terminatebefore a reaction would otherwise reach a plateau. In some embodiments,terminating amplification before reaching a plateau can minimizeamplification of polynucleotides that are most abundant in a sample.Therefore, in some embodiments, an equivalent number of multiplexamplicons from various polynucleotide can be produced irrespective ofthe starting copy number of the various polynucleotides. In someembodiments, terminating a PCR reaction before a plateau can be achievedusing a limiting and equivalent number of amplification primer pairs foreach target polynucleotide to be analyzed (see, e.g., U.S. ApplicationSer. No. 60/584,665).

In some embodiments, multiplex amplicons can be produced by PCR asdescribed in U.S. Patent Application No. 20040175733, incorporated byreference. Therefore, in some embodiments, the conditions of multiplexamplification can include a concentration of thermostable polymerase,such as, AMPLITAQ GOLD™ DNA polymerase (Applied Biosystems, AppleraCorp., Foster City, Calif.) from about 2 U/20 μl to about 16 U/20 μl,from about 2 U/20 μl to about 9 U/20 μl, from about 2 U/20 μl to about 6U/20 μl, from about 7 U/20 μl to about 16 U/20 μl, or from about 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 U/20 μl reaction volume.In some embodiments, primer extension can be for about 2, 3, 4, 5, 6, 7,8, 9, 10 min., or even longer. In some embodiments, multiplexamplification primers can be used at concentrations in the range ofabout 30-900 nM each primer. Different amplification primer pairs may bepresent at different concentrations within this range or, alternatively,some or all of the multiplex amplification primers may be present atapproximately equimolar concentrations within this range. In someembodiments, at least some of the multiplex amplification primers, forexample, approximately 10%, 25%, 35%, 50%, 60%, or more, can be presentin approximately equimolar concentrations ranging from about 30 nM toabout 100 nM each primer. In some embodiments, all of the multiplexamplification primers can be present at approximately equimolarconcentrations in the range of about 30 nM to about 100 nM each primer.In some embodiments, all of the amplification primers can be present atconcentrations of about 10, 20, 30, 40, 45, 50, 60, 70, 80, 90, 100,200, 300, 400, 500, 600, 700, 800 or 900 nM each primer. In someembodiments, some or all of the amplification primers can be present ina concentration of about 45 μM each primer. The amplification primerconcentrations discussed above can be used regardless of whether thetarget polynucleotide(s) being amplified are RNA or DNA. In someembodiments, the number of primer pairs can be at least 100, 200, 300,400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000,8000, 9000, 10000, 15000, 20000, 25000 or up to about 30000. Inaddition, in embodiments wherein targeted polynucleotides are RNA, thereverse-transcription reaction of a multiplex RT-PCR amplification workswell at the stated primer concentrations.

The number of multiplex amplification cycles performed may depend upon,among other factors, the degree of amplification desired, which maydepend upon such factors as the amount of polynucleotide to be multiplexamplified and/or the intended method of clonal amplification andanalysis. Accordingly, the number of cycles employed can vary fordifferent applications and will be apparent to those of skill in theart. For most applications, multiplex amplification reactions carriedout for about 10 amplification cycles can be expected to yieldsufficient amplification product even when the sample is of limitedquantity (e.g., 1 to a few cells), a polynucleotide of interest ispresent in very low copy number, and/or is present only as a singlecopy, regardless of the amount of sample required to perform theanalysis. However, more or fewer multiplex amplification cycles may beemployed. In some embodiments multiplex amplification can be carried outfor as many as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, or more cycles. In some embodiments, multiplexamplification can be carried out for 2-12 cycles, inclusive, for 5-11cycles, inclusive, or for up to 14 cycles, inclusive.

In addition to sequences suitable for priming multiplex amplification ofpolynucleotides, one or more multiplex amplification primers can bedesigned to introduce sequences into multiplex amplicons that can beused to facilitate isolation, clonal amplification, and analysis.However, the skilled artisan will appreciated that other types ofsequences also can be introduced into multiplex amplicons, such as,enhancers, promoters, restriction endonuclease sites, etc. In someembodiments, a sequence introduced into a multiplex amplicon may be acode sequence which may be used as a surrogate or marker for eachmultiplex amplicon. Therefore, each “code sequence” is substantiallyunique and can be used to identify or distinguish the polynucleotidecomprising the code sequence (see, e.g., U.S. Application Ser. Nos.60/584,596; 60/584,621; 60/584,643; 60/584,665). In some embodiments, amultiplex amplification primer sequence may be shared by at least oneother amplicon. For example, in some embodiments, a sequence may becommon to each forward amplification primer or each reverseamplification primer. Thus, “forward universal sequence” and “reverseuniversal sequence” refer to multiplex amplification primer sequencesshared by each forward or reverse primer, respectively. As exemplifiedin FIG. 1, forward primer 10 and reverse primer 20 comprisepolynucleotide 1 specific sequences 15 and 25, respectively. 5′ relativeto polynucleotide 1 specific sequences, forward primer 10 and reverseprimer 20 comprise universal forward sequence 30 and universal reversesequence 40, respectively, which are incorporated into amplicon 50.Therefore, when amplicon 50 is isolated, for example, in a hydrophiliccompartment, the universal forward and reverse can be used as primersites for clonal amplification or analysis.

In some embodiments, code, universal, and/or other types of sequencescan be added to a polynucleotide or multiplex amplicons using linkersand/or adaptors (Sambrook et al., Molecular Cloning: A Laboratory Manual1.84, 1.88-1.89, 1.98-1.102, 1.160-1.161, 11.20-11.21, 11.51-11.55,11.102 (3d. ed. Cold Spring Harbor Laboratory Press). For example, insome embodiments, a polynucleotide can be sheared, restriction enzymedigested, or treated with a polymerase or kinase to prepare the terminiof a polynucleotide for the addition of linkers and/or adaptors. In someembodiments, sequences, including those described above, can be added toa polynucleotide by homologous recombination using RecA and/or otherrecombinases (see, e.g., U.S. Pat. Nos. 4,888,274, 5,989,879, 6,090,539,6,074,853, 6,200,812, 6,391,564, 6,524,856). Determining the number,type, length, and composition of the various sequences and theirdistribution or commonality among polynucleotides or multiplex ampliconsemployed, including incorporation of sequences into amplificationprimers and amplicons derived therefrom are known in the art. (see,e.g., U.S. Pat. Nos. 5,314,809, 5,853,989, 5,882,856, 6,090,552,6,355,431, 6,617,138, 6,630,329, 6,635,419, 6,670,130, 6,670,161; andWeighardt et al., 1993, PCR Methods and App. 3:77, the disclosures ofwhich are incorporated by reference).

As will be appreciated by skilled artisans, @polynucleotides suitablefor analysis by the disclosed methods may be either DNA (e.g, cDNA,genomic DNA, extrachromosomal DNA (e.g. mitochondrial DNA, plasmid DNA),an amplicon) or RNA (e.g., mRNA, rRNA, tRNA, an in vitro transcript, orgenomic RNA (e.g., virion RNA (vRNA)) in nature, and may be derived orobtained from virtually any sample or source (e.g., human, non-human,plant, animal, microorganism etc.), wherein the sample may optionally bescarce or of a limited quantity. For example, the sample may be one or afew cells collected from a crime scene or a small amount of tissuecollected via biopsy. In some embodiments, the target polynucleotide maybe a synthetic polynucleotide comprising nucleotide analogs or mimics,as described below, produced for purposes, such as, diagnosis, testing,or treatment.

In various non-limiting examples, polynucleotide suitable for analysismay be single or double-stranded, or a combination thereof, linear orcircular, a chromosome or a gene or a portion or fragment thereof, aregulatory polynucleotide, a restriction fragment from, for example, aplasmid or chromosomal DNA, genomic DNA, mitochondrial DNA, DNA from aconstruct or library of constructs (e.g., from a YAC, BAC or PAClibrary), RNA (e.g, mRNA, rRNA or vRNA) or a cDNA or a cDNA library. Asknown in the art, a cDNA is a single- or double-stranded DNA produced byreverse transcription of an RNA template. Therefore, some embodimentsinclude a reverse transcriptase and one or more primers suitable forreverse transcribing an RNA template into a cDNA. Reactions, reagentsand conditions for carrying out such “RT” reactions are known in the art(see, e.g., Blain et al., 1993, J. Biol. Chem. 5:23585-23592; Blain etal., 1995, J. Virol. 69:4440-4452; PCR Essential Techniques 61-63,80-81, (Burke, ed., J. Wiley & Sons 1996); Gubler et al., 1983, Gene25:263-269; Gubler, 1987, Methods Enzymol., 152:330-335; Sellner et al.,1994, J. Virol. Method. 49:47-58; Okayama et al., 1982, Mol. Cell. Biol.2:161-170; and U.S. Pat. Nos. 5,310,652, 5,322,770, and 6,300,073, thesedisclosures of which are incorporated herein by reference. In someembodiments, a polynucleotide may include a single polynucleotide (e.g.,a chromosome, plasmid) from which one or more different sequences ofinterest may be optionally selected, clonally amplified, and analyzed.

In some embodiments, clonal amplicons can be analyzed by virtually anymethod selected at the discretion of the practitioner. Therefore,reactions comprising any one or more steps of probe or primerhybridization, primer extension, labeling, etc. can be used to detect,quantitate, and/or determine the composition of clonal amplicons. Forexample, in some embodiments, the transcriptome of one or more genomescan be amplified by multiplex PCR, as described above, whereby forwardand reverse universal amplicons can be incorporated into each amplicon.In some embodiments, the multiplex amplicons can be isolated, forexample, in hydrophilic compartments of an inverse emulsion, andclonally amplified using primers comprising the forward and reverseuniversal sequences. In some embodiments, one of the clonalamplification primers can be attached to a surface as exemplified inFIG. 3 to produce isolated populations of clonal amplicons asexemplified in FIG. 4.

In some embodiments, clonal amplicons can be analyzed in a parallelmanner. Without being bound by theory, because the clonal amplicons thatare produced are isolated as discrete populations, the clonal ampliconscan be analyzed in parallel. For example, as shown in FIG. 4, thediscrete populations of clonal amplicons can be analyzed in parallel asa result of their attachment to discrete areas of a surface. Therefore,in some embodiments, at least at least 100, 500, 1000, 10000, 50000,100000, 300000, 500000, or 1000000 populations of clonal amplicons canbe analyzed in parallel. The skilled artisan will appreciate thatvarious methods can be suitable for parallel analysis of clonalamplicons. Generally, such methods can produce a discrete detectablesignal that can be associated or linked to individual populations ofclonal amplicons.

In some embodiments, clonal amplicons can be sequenced using sequencingtechniques based on sequencing-by-synthesis techniques. For example, insome embodiments the enzymatic method of Sanger et al. 1977, Proc. Natl.Acad. Sci., 74: 5463-5467, can be employed. The Sanger technique usescontrolled synthesis of nucleic acids to generate fragments thatterminate at specific points along the sequence of interest. Techniquesbased on the Sanger method typically begin by annealing a syntheticsequencing primer to a nucleic acid template (e.g., targetpolynucleotide or amplicon). The primer can be extended in the presenceof four dNTPs (i.e., dGTP, dCTP, dATP and dTTP) and small proportion offour 2′,3′-ddNTPs that carry a 3′-H atom on the deoxyribose moiety,rather than the conventional 3′-OH group. Incorporation of a ddNTPmolecule into the growing DNA chain prevents formation of aphosphodiester bond with the succeeding dNTP, thus, extension of thegrowing chain can be terminated. The products of the reaction are anested set of oligonucleotide chains with co-terminal 5′ termini andwhose lengths are determined by the distance between the 5′ terminus ofthe primer used to initiate DNA synthesis and the sites of ddNTP chaintermination. These populations of oligonucleotides can be separated byelectrophoresis and the sequence of the template DNA determined (see,e.g., U.S. Pat. Nos. 4,994,372, 5,332,666, 5,498,523, 5,800,996,5,821,058, 5,863,727, 5,945,526, and 6,258,568; and Sanger et al., 1972,Proc. Natl. Acad. Sci. USA, 74: 5463-5467; and Sanger, 1981, Science,214: 1205-1210).

Based on the labeling strategy used to identify the bases, describedbelow, sequencing reactions can be performed in parallel. For example,in some embodiments distinguishable labels can be attached to eachddNTP. Therefore, a single extension/termination reaction can be usedwhich contains the four ddNTPs, each comprising a spectrally resolvablelabel. Suitable spectrally resolvable labels include but are not limitedfluorophores. (see, e.g., U.S. Pat. Nos. 5,821,058, 5,332,666, and5,945,526.)

In some embodiments, a method of sequencing based on the detection ofbase incorporation by the release of a pyrophosphate and simultaneousenzymatic nucleotide degradation can be used (see, e.g., U.S. Pat. No.6,258,568). For example, clonal amplicons can be sequenced using aprimer and adding four different dNTPs or ddNTPs subjected to apolymerase reaction. As each dNTP or ddNTP is added to the primerextension product, a pyrophosphate molecule is released. Pyrophosphaterelease can be detected enzymatically, such as, by the generation oflight in a luciferase-luciferin reaction (see, e.g., WO 93/23564 and WO89/09283). Additionally, a nucleotide degrading enzyme, such as apyrase,can be present during the reaction in order to degrade unincorporatednucleotides (see, e.g., U.S. Pat. No. 6,258,568; hereby incorporated byreference in its entirety). In other embodiments, the reaction can becarried out in the presence of a sequencing primer, polymerase, anucleotide degrading enzyme, deoxynucleotide triphosphates, and apyrophosphate detection system comprising ATP sulfurylase and luciferase(see, e.g., U.S. Pat. No. 6,258,568).

In some embodiments, a method of sequencing can be fluorescent in situsequencing (FISSEQ). In FISSEQ, a primer can be extended by adding afluorescently-labeled dNTP followed by washing away of unincorporateddNTP. The incorporated dNTP can be detected by fluorescence. At eachcycle, the fluorescence from previous cycles can be “bleached” ordigitally subtracted. (Mitra et al., 2003, Analytical Biochemistry320:55-65; Zhu et al., 2003, Science 301:836-8; U.S. Application Nos.20020120126, 20020120127, 20020127552, 20030099972, 20030124594, and20030207265). In some embodiments, a method of sequencing can behybridization sequencing (see, e.g., Baines et al., 1988, J. Theor.Biol. 135(3):303-7; Drmanac et al., Genomics 4(2):114-28; Khrapko etal., 1989, FEBS Lett. 256(1-2):118-22; Lysov et al.,1988, Dokl Akad NaukSSSR. 303(6):1508-11; Pevzner, 1989, J. Biomol. Struct. Dyn.7(1):63-73); Southern et al., 1992, Genomics 13(4):1008-17).

In some embodiments, clonal amplicons attached to a solid support can besequenced. For example, clonal amplicons attached to a microparticleproduced in a hydrophilic compartment can be collected en masse bybreaking the emulsion, distributed into individual wells of a multi-wellplate, and sequenced. In some embodiments, clonal amplicons attached toa surface of a slide can be sequenced in a parallel reaction.

In some embodiments, clonal amplicons can be sequenced by massivelyparallel signature sequencing (MPSS) which comprises two techniques: onefor tagging and sorting fragments of DNA for parallel processing, andanother for the stepwise sequencing the end of a DNA fragment. MPSS isdescribed in U.S. Pat. Nos. 5,599,675, 5,695,934, 5,714,330, 5,763,175,5,831,065. 5,863,722, 6,013,445, 6,172,214, 6,511,802; U.S. PatentApplication Nos. 20040038283, 20040002104, 20030077615; andInternational Appl. Nos. PCT/US96/09513, PCT/US97/09472. In someembodiments, MPSS can be carried out by ligating an encoded adaptor toan end of a polynucleotide to be sequenced, the encoded adaptor having anuclease recognition site of a nuclease whose cleavage site is separatefrom its recognition site; identifying one or more nucleotides at theend of the fragment by the identity of the encoded adaptor ligatedthereto, cleaving the polynucleotide with a nuclease recognizing thenuclease recognition site of the encoded adaptor such that thepolynucleotide is shortened by one or more nucleotides; and repeatingthe steps until the nucleotide sequence of the end of the polynucleotidecan be determined. (U.S. Pat. No. 6,511,802)

A variety of nucleic acid polymerases may be used in the methodsdescribed herein. For example, the nucleic acid polymerizing enzyme canbe a thermostable polymerase or a thermally degradable polymerase.Suitable thermostable polymerases include, but are not limited to,polymerases isolated from Thermus aquaticus, Thermus thermophilus,Pyrococcus woesei, Pyrococcus furiosus, Thermococcus litoralis, andThermotoga maritima. Therefore, in some embodiments, “cycle sequencing”can be performed. Suitable thermodegradable polymersases include, butare not limited to, E. coli DNA polymerase I, the Klenow fragment of E.coli DNA polymerase I, T4 DNA polymerase, T5 DNA polymerase, T7 DNApolymerase, and others. Examples of other polymerizing enzymes that canbe used in the methods described herein include but are not limited toT7, T3, SP6 RNA polymerases and AMV, M-MLV and HIV reversetranscriptases.

Non-limiting examples of commercially available polymerases that can beused in the methods described herein include, but are not limited to,TaqFS®, AmpliTaq CS (Perkin-Elmer), AmpliTaq FS (Perkin-Elmer), Kentaq1(AB Peptide, St. Louis, Mo.), Taquenase (Scien Tech Corp., St. Louis,Mo.), ThermoSequenase (Amersham), Bst polymerase, Vent_(R)(exo⁻) DNApolymerase, Reader™Taq DNA polymerase, VENT™ DNA polymerase (New EnglandBiolabs), DEEPVENT™ DNA polymerase (New England Biolabs), PFUTurbo™ DNApolymerase (Stratagene), Tth DNA polymerase, KlenTaq-1 polymerase,SEQUENASE™ 1.0 DNA polymerase (Amersham Biosciences), and SEQUENASE 2.0DNA polymerase (United States Biochemicals).

The products of sequencing reactions can be analyzed by a wide varietyof methods. For example, the products can be separated by asize-dependent process, e.g., gel electrophoresis, capillaryelectrophoresis (CE: e.g., 3730 DNA Analyzer, 3730x1 DNA Analyzer,3100-Avant genetic analyser, and 270A-HT Capillary Electrophoresissystem (Applied Biosystems, Foster City, Calif.)) (see, e.g., U.S. Pat.Nos. RE37941, 5,384,024, 6,372,106, 6,372,484, 6,387,234, 6,387,236,6,402,918, 6,402,919, 6,432,651, 6,462,816, 6,475,361, 6,476,118,6,485,626, 6,531,041, 6,544,396, 6,576,105, 6,592,733, 6,596,140,6,613,212, 6,635,164, and 6,706,162) using various polymers (e.g.,separation polymer (e.g., POP-4™ POP-6™, or POP-7™ (Applied Biosystems,Foster City, Calif.), linear polyacrylamide (LPA: Klepamik et al., 2001,Electrophoresis 22(4):783-8; Kotler et al., 2002, Electrophoresis23(17):3062-70; Manabe et al., 1998, Electrophoresis 19:2308-2316)),chromatography, thin layer chromatography, or paper chromatography. Theseparated fragments can be detected, e.g., by laser-induced fluorescence(see, e.g., U.S. Pat. Nos. 5,945,526, 5,863,727, 5,821,058, 5,800,996,5,332,666, 5,633,129, and 6,395,486), autoradiagraphy, orchemiluminescence. In some embodiments, the products of the sequencingreaction can be separated using gel electrophoresis and visualized usingstains such as ethidium bromide or silver stain. The reaction productscan also be analyzed by mass spectrometric methods (see, e.g., U.S. Pat.Nos. 6,225,450 and 5,104,12). In some embodiments, products of thesequencing reaction can be analyzed using microfluidic systems,including but not limited to microcapillary electrophoretic systems andmethods (see, e.g., Doherty et al., 2004, Analytical Chemistry76:5249-5256; Ertl et al., 2004, Analytical Chemistry 76:3749-3755; Haabet al., 1999, Analytical Chemistry 71:5137-5145 (1999); Kheterpal etal., 1999, Analytical Chemistry 71:31A-37A; Lagally et al., 2000,Sensors and Actuators B 63:138-146; Lagally et al., 2001, Anal. Chem.73:565-570; Lagally et al., 2003, Genetic Analysis Using a PortablePCR-CE Microsystem, in Micro Total Analysis Systems Vol. 2, Northrup etal. (eds.) pp. 1283-1286; Liu et al., 1999, Anal. Chem. 71:566-573;Medintz et al., 2000, Electrophoresis 21:2352-2358; Medintz et al.,2001, Genome Research 11:413-421; Paegel et al., Current Opinions inBiotechnology 14:42-50; Scherer et al., 1999, Electrophoresis20:1508-1517; Shi et al., 1999, Analytical Chemistry 71:5354-5361;Wedemayer et al., 2001, BioTechniques 30:122-128; U.S. Pat. Nos.6,787,015, 6,787,016; U.S. Application Nos. 20020166768, 20020192719,20020029968, 20030036080, 20030087300, 20030104466, 20040045827,20040096960; EP1305615; and WO 02/08744).

The various primers (e.g., multiplex amplification, clonalamplification, and/or sequencing), generally, should be sufficientlylong to prime template-directed synthesis under the conditions of thereaction. The exact lengths of the primers may depend on many factors,including but not limited to, the desired hybridization temperaturebetween the primers and polynucleotides, the complexity of the differenttarget polynucleotide sequences, the salt concentration, ionic strength,pH and other buffer conditions, and the sequences of the primers andpolynucleotides. The ability to select lengths and sequences of primerssuitable for particular applications is within the capabilities ofordinarily skilled artisans (see, e.g., Sambrook et al. MolecularCloning: A Laboratory Manual 9.50-9.51, 11.46, 11.50 (2d. ed., ColdSpring Harbor Laboratory Press); Sambrook et al., Molecular Cloning: ALaboratory Manual 10.1-10.10 (3d. ed. Cold Spring Harbor LaboratoryPress)). In some embodiments, the primers contain from about 15 to about35 nucleotides that are suitable for hybridizing to a targetpolynucleotide and form a substrate suitable for DNA synthesis, althoughthe primers may contain more or fewer nucleotides. Shorter primersgenerally require lower temperatures to form sufficiently stable hybridcomplexes with target sequences. The capability of polynucleotides toanneal can be determined by the melting temperature (“T_(m)”) of thehybrid complex. T_(m) is the temperature at which 50% of apolynucleotide strand and its perfect complement form a double-strandedpolynucleotide. Therefore, the T_(m) for a selected polynucleotidevaries with factors that influence or affect hybridization. In someembodiments, in which thermocycling occurs, the primers can be designedto have a melting temperature (“T_(m)”) in the range of about 60-75° C.Melting temperatures in this range tend to insure that the primersremain annealed or hybridized to the target polynucleotide at theinitiation of primer extension. The actual temperature used for a primerextension reaction may depend upon, among other factors, for example,the concentration of the primers. For reactions carried out with athermostable polymerase such as Taq DNA polymerase, in exemplaryembodiments primers can be designed to have a T_(m) in the range ofabout 60 to about 78° C. or from about 55 to about 70° C. The meltingtemperatures of the different primers can be different; however, in analternative embodiment they should all be approximately the same, i.e.,the T_(m) of each primer, for example, in a parallel reaction can bewithin a range of about 5° C. or less. The T_(m)s of various primers canbe determined empirically utilizing melting techniques that arewell-known in the art (see, e.g., Sambrook et al. Molecular Cloning: ALaboratory Manual 11.55-11.57 (2d. ed., Cold Spring Harbor LaboratoryPress)). Alternatively, the T_(m) of a primer can be calculated.Numerous references and aids for calculating T_(ms) of primers areavailable in the art and include, by way of example and not limitation,Baldino et al. Methods Enzymology. 168:761-777; Bolton et al., 1962,Proc. Natl. Acad. Sci. USA 48:1390; Bresslauer et al., 1986, Proc. Natl.Acad. Sci. USA 83:8893-8897; Freier et al., 1986, Proc. Natl. Acad. Sci.USA 83:9373-9377; Kierzek et al., Biochemistry 25:7840-7846; Montpetitet al., 1992, J. Virol. Methods 36:119-128; Osborne, 1991, CABIOS 8:83;Rychlik et al., 1990, Nucleic Acids Res. 18:6409-6412 (erratum, 1991,Nucleic Acids Res. 19:698); Rychlik. J. NIH Res. 6:78; Sambrook et al.Molecular Cloning: A Laboratory Manual 9.50-9.51, 11.46-11.49 (2d. ed.,Cold Spring Harbor Laboratory Press); Sambrook et al., MolecularCloning: A Laboratory Manual 10.1-10.10 (3d. ed. Cold Spring HarborLaboratory Press)); SantaLucia, 1998, Proc. Natl. Acad. Sci. USA95:1460-1465; Suggs et al., 1981, In Developmental Biology UsingPurified Genes (Brown et al., eds.), pp. 683-693, Academic Press;Wetmur, 1991, Crit. Rev. Biochem. Mol. Biol. 26:227-259, whichdisclosures are incorporated by reference. Any of these methods can beused to determine a T_(m) of a primer.

As the skilled artisan will appreciate, in general, the relativestability and therefore, the T_(m)s, of RNA:RNA, RNA:DNA, and DNA:DNAhybrids having identical sequences for each strand may differ. Ingeneral, RNA:RNA hybrids are the most stable (highest relative T_(m))and DNA:DNA hybrids are the least stable (lowest relative T_(m)).Accordingly, in some embodiments, another factor to consider, inaddition to those described above, when designing a primer is thestructure of the primer and target polynucleotide. For example, in theembodiment in which an RNA polynucleotide is reverse transcribed toproduce a cDNA, the determination of the suitability of a DNA primer forthe reverse transcription reaction should include the effect of the RNApolynucleotide on the T_(m) of the primer. Although the T_(m)s ofvarious hybrids may be determined empirically, as described above,examples of methods of calculating the T_(m) of various hybrids arefound at Sambrook et al. Molecular Cloning: A Laboratory Manual 9.51(2d. ed., Cold Spring Harbor Laboratory Press).

The sequences of primers useful for the disclosed methods are designedto be substantially complementary to regions of the targetpolynucleotides. By “substantially complementary” herein is meant thatthe sequences of the primers include enough complementarity to hybridizeto the target polynucleotides at the concentration and under thetemperature and conditions employed in the reaction and to be extendedby the DNA polymerase.

In some embodiments, primers can be a nucleobase polymer. By“nucleobase” is meant naturally occurring and synthetic heterocyclicmoieties commonly known to those who utilize nucleic acid orpolynucleotide technology or utilize polyamide or peptide nucleic acidtechnology to generate polymers that can hybridize to polynucleotides ina sequence-specific manner. Non-limiting examples of suitablenucleobases include: adenine, cytosine, guanine, thymine, uracil,5-propynyl-uracil, 2-thio-5-propynyl-uracil, 5-methylcytosine,pseudoisocytosine, 2-thiouracil and 2-thiothymine, 2-aminopurine,N9-(2-amino-6-chloropurine), N9-(2,6-diaminopurine), hypoxanthine,N9-(7-deaza-guanine), N9-(7-deaza-8-aza-guanine) andN8-(7-deaza-8-aza-adenine). Other non-limiting examples of suitablenucleobases include those nucleobases disclosed in FIGS. 2(A) and 2(B)of Buchardt et al. (U.S. Pat. No. 6,357,163; WO 92/20702 and WO92/20703).

The skilled artisan will appreciate that the suitability of anynucleobase used in a primer can depend, at least in part, on theintended use of the primer. For example, a nucleobase suitable for asequencing primer may not be suitable as a multiplex amplification orclonal amplification primer. This is because particular nucleobases maynot provide a suitable template for a polymerase. For example,peptide-nucleic acids (PNAs), described below, do not provide a suitabletemplate for polymerases. Therefore, primers comprising one or morePNAs, are generally, not suitable for exponential amplifications by PCRbecause DNA synthesis ceases when a thermostable polymerase encountersthe PNA in the template strand. However, primers comprising PNA can besuitable for sequencing reactions and amplification reactions that donot require a polymerase to read through the PNA, including but notlimited to, linear PCR amplifications. Determining the types ofnucleobases suitable for primers employed in the various types ofamplification and analysis reactions as disclosed herein is within theabilities of the skilled artisan.

Nucleobases can be linked to other moieties to form nucleosides,nucleotides, and nucleoside/tide analogs. As used herein, “nucleoside”refers to a compound consisting of a purine, deazapurine, or pyrimidinenucleoside base, e.g., adenine, guanine, cytosine, uracil, thymine,7-deazaadenine, 7-deazaguanosine, that is linked to the anomeric carbonof a pentose sugar at the 1′ position, such as a ribose, 2′-deoxyribose,or a 2′,3′-di-deoxyribose. When the nucleoside base is purine or7-deazapurine, the pentose is attached at the 9-position of the purineor deazapurine, and when the nucleoside base is pyrimidine, the pentoseis attached at the 1-position of the pyrimidine (see, e.g., Kornberg andBaker, DNA Replication, 2nd Ed. (Freeman 1992)). The term “nucleotide”as used herein refers to a phosphate ester of a nucleoside, e.g., amono-, a di-, or a triphosphate ester, wherein the most common site ofesterification is the hydroxyl group attached to the C-5 position of thepentose. “Nucleotide 5′-triphosphate” refers to a nucleotide with atriphosphate ester group at the 5′ position. The term “nucleoside/tide”as used herein refers to a set of compounds including both nucleosidesand/or nucleotides.

“Nucleobase polymer or oligomer” refers to two or more nucleobasesconnected by linkages that permit the resultant nucleobase polymer oroligomer to hybridize to a polynucleotide having a complementarynucleobase sequence. Nucleobase polymers or oligomers include, but arenot limited to, poly- and oligonucleotides (e.g., DNA and RNA polymersand oligomers), poly- and oligonucleotide analogs and poly- andoligonucleotide mimics, such as polyamide or peptide nucleic acids.Nucleobase polymers or oligomers can vary in size from a fewnucleobases, from 2 to 40 nucleobases, to several hundred nucleobases,to several thousand nucleobases, or more.

“Polynucleotide or oligonucleotide” refers to nucleobase polymers oroligomers in which the nucleobases are connected by sugar phosphatelinkages (sugar-phosphate backbone). Exemplary poly- andoligonucleotides include polymers of 2′-deoxyribonucleotides (DNA) andpolymers of ribonucleotides (RNA). A polynucleotide may be composedentirely of ribonucleotides, entirely of 2′-deoxyribonucleotides orcombinations thereof.

In some embodiments, a nucleobase polymer is an polynucleotide analog oran oligonucleotide analog. By “polynucleotide analog or oligonucleotideanalog” is meant nucleobase polymers or oligomers in which thenucleobases are connected by a sugar phosphate backbone comprising oneor more sugar phosphate analogs. Typical sugar phosphate analogsinclude, but are not limited to, sugar alkylphosphonates, sugarphosphoramidites, sugar alkyl- or substituted alkylphosphotriesters,sugar phosphorothioates, sugar phosphorodithioates, sugar phosphates andsugar phosphate analogs in which the sugar is other than 2′-deoxyriboseor ribose, nucleobase polymers having positively charged sugar-guanidylinterlinkages such as those described in U.S. Pat. No. 6,013,785 andU.S. Pat. No. 5,696,253 (see also, Dagani, 1995, Chem. & Eng. News4-5:1153; Dempey et al., 1995, J. Am. Chem. Soc. 117:6140-6141). Suchpositively charged analogues in which the sugar is 2′-deoxyribose arereferred to as “DNGs,” whereas those in which the sugar is ribose arereferred to as “RNGs.” Specifically included within the definition ofpoly- and oligonucleotide analogs are locked nucleic acids (LNAs; see,e.g., Elayadi et al., 2002, Biochemistry 41:9973-9981; Koshkin et al.,1998, J. Am. Chem. Soc. 120:13252-3; Koshkin et al., 1998, TetrahedronLetters, 39:4381-4384; Jumar et al., 1998, Bioorganic & MedicinalChemistry Letters 8:2219-2222; Singh and Wengel, 1998, Chem. Commun.,12:1247-1248; WO 00/56746; WO 02/28875; and, WO 01/48190.

In some embodiments, a nucleobase polymer is a polynucleotide mimic oroligonucleotide mimic. “Polynucleotide mimic or oligonucleotide mimic”refers to a nucleobase polymer or oligomer in which one or more of thebackbone sugar-phosphate linkages is replaced with a sugar-phosphateanalog. Such mimics are capable of hybridizing to complementarypolynucleotides or oligonucleotides, or polynucleotide oroligonucleotide analogs or to other polynucleotide or oligonucleotidemimics, and may include backbones comprising one or more of thefollowing linkages: positively charged polyamide backbone withalkylamine side chains as described in U.S. Pat. Nos. 5,786,461,5,766,855, 5,719,262, 5,539,082 and WO 98/03542 (see also, Haaima etal., 1996, Angewandte Chemie Int'l Ed. in English 35:1939-1942; Lesnicket al., 1997, Nucleotid. 16:1775-1779; D'Costa et al., 1999, Org. Lett.1:1513-1516; Nielsen, 1999, Curr. Opin. Biotechnol. 10:71-75); unchargedpolyamide backbones as described in WO 92/20702 and U.S. Pat. No.5,539,082; uncharged morpholino-phosphoramidate backbones as describedin U.S. Pat. Nos. 5,698,685, 5,470,974, 5,378,841, and 5,185,144 (seealso, Wages et al., 1997, BioTechniques 23:1116-1121); peptide-basednucleic acid mimic backbones (see, e.g., U.S. Pat. No. 5,698,685);carbamate backbones (see, e.g, Stirchak and Summerton, 1987, J. Org.Chem. 52:4202); amide backbones (see, e.g., Lebreton, 1994, Synlett.February, 1994:137); methylhydroxylamine backbones (see, e.g., Vasseuret al., 1992, J. Am. Chem. Soc. 114:4006); 3′-thioformacetal backbones(see, e.g., Jones et al., 1993, J. Org. Chem. 58:2983) and sulfamatebackbones (see, e.g., U.S. Pat. No. 5,470,967). All of the precedingreferences are herein incorporated by reference.

“Peptide nucleic acid” or “PNA” refers to poly- or oligonucleotidemimics in which the nucleobases are connected by amino linkages(uncharged polyamide backbone) such as described in any one or more ofU.S. Pat. Nos. 5,539,082, 5,527,675, 5,623,049, 5,714,331, 5,718,262,5,736,336, 5,773,571, 5,766,855, 5,786,461, 5,837,459, 5,891,625,5,972,610, 5,986,053, 6,107,470, 6,451,968, 6,441,130, 6,414,112 and6,403,763; all of which are incorporated herein by reference. The term“peptide nucleic acid” or “PNA” shall also apply to any oligomer orpolymer comprising two or more subunits of those polynucleotide mimicsdescribed in the following publications: Lagriffoul et al., 1994,Bioorganic & Medicinal Chemistry Letters, 4:1081-1082; Petersen et al.,1996, Bioorganic & Medicinal Chemistry Letters, 6:793-796; Diderichsenet al., 1996, Tett. Lett. 37:475-478; Fujii et al., 1997, Bioorg. Med.Chem. Lett. 7:637-627; Jordan et al., 1997, Bioorg. Med. Chem. Lett.7:687-690; Krotz et al., 1995, Tett. Lett. 36:6941-6944; Lagriffoul etal., 1994, Bioorg. Med. Chem. Lett. 4:1081-1082; Diederichsen, 1997,Bioorg. Med. Chem. 25 Letters, 7:1743-1746; Lowe et al., 1997, J. Chem.Soc. Perkin Trans. 1, 1:539-546; Lowe et al., 1997, J. Chem. Soc. PerkinTrans. 11:547-554; Lowe et al., 1997, I. Chem. Soc. Perkin Trans. 11:555-560; Howarth et al., 1997, I. Org. Chem. 62:5441-5450; Altmann etal., 1997, Bioorg. Med. Chem. Lett., 7:1119-1122; Diederichsen, 1998,Bioorg. Med. Chem. Lett., 8:165-168; Diederichsen et al., 1998, Angew.Chem. mt. Ed., 37:302-305; Cantin et al., 1997, Tett. Lett.,38:4211-4214; Ciapetti et al., 1997, Tetrahedron, 53:1167-1176;Lagriffoule et al., 1997, Chem. Eur. 1. 3:912-919; Kumar et al., 2001,Organic Letters 3(9):1269-1272; and the Peptide-Based Nucleic AcidMimics (PENAMs) of Shah et al. as disclosed in WO 96/04000.

Some examples of PNAs are those in which the nucleobases are attached toan N-(2-aminoethyl)-glycine backbone, i.e., a peptide-like, amide-linkedunit (see, e.g., U.S. Pat. No. 5,719,262; Buchardt et al., 1992, WO92/20702; Nielsen et al., 1991, Science 254:1497-1500).

In some embodiments, a nucleobase polymer is a chimeric oligonucleotide.By “chimeric oligonucleotide” is meant a nucleobase polymer or oligomercomprising a plurality of different polynucleotides, polynucleotideanalogs and polynucleotide mimics. For example a chimeric oligo maycomprise a sequence of DNA linked to a sequence of RNA. Other examplesof chimeric oligonucleotides include a sequence of DNA linked to asequence of PNA, and a sequence of RNA linked to a sequence of PNA.

In some embodiments, various components of the disclosed methods,including but not limited to primers, ddNTPs, and the reactioncompartments, can comprise a detectable moiety. “Detectable moiety,”“detection moiety” or “label” refer to a moiety that renders a moleculeto which it is attached detectable or identifiable using known detectionsystems (e.g., spectroscopic, radioactive, enzymatic, chemical,photochemical, biochemical, immunochemical, chromatographic, physical(e.g., sedimentation, centrifugation, density), electrophoretic,gravimetric, or magnetic systems). Non-limiting examples of labelsinclude quantum dots, isotopic labels (e.g., radioactive or heavyisotopes), magnetic labels; spin labels, electric labels; thermallabels; colored labels (e.g., chromophores), luminescent labels (e.g.,fluorescers, chemiluminescers), enzyme labels (e.g., horseradishperoxidase, alkaline phosphatase, luciferase, β-galactosidase) (Ichiki,et al., 1993, J. Immunol. 150(12):5408-5417; Nolan, et al., 1988, Proc.Natl. Acad. Sci. USA 85(8):2603-2607)), antibody labels, and chemicallymodifiable labels. In addition, in some embodiments, such labels includecomponents of ligand-binding partner pairs (e.g., antigen-antibody(including single-chain antibodies and antibody fragments, e.g., FAb,F(ab)′₂, Fab′, Fv, etc. (Fundamental Immunology 47-105 (William E. Pauled., 5^(th) ed., Lippincott Williams & Wilkins 2003)), hormone-receptorbinding, neurotransmitter-receptor binding, polymerase-promoter binding,substrate-enzyme binding, inhibitor-enzyme binding (e.g.,sulforhodamine-valyl-alanyl-aspartyl-fluoromethylketone(SR-VAD-FMK-caspase(s) binding), allosteric effector-enzyme binding,biotin-streptavidin binding, digoxin-antidigoxin binding,carbohydrate-lectin binding, Annexin V-phosphatidylserine binding(Andree et al., 1990, J. Biol. Chem. 265(9):4923-8; van Heerde et al.,1995, Thromb. Haemost. 73(2):172-9; Tait et al., 1989, J. Biol. Chem.264(14):7944-9), nucleic acid annealing or hybridization, or a moleculethat donates or accepts a pair of electrons to form a coordinatecovalent bond with the central metal atom of a coordination complex. Invarious exemplary embodiments the dissociation constant of the bindingligand can be less than about 10⁻⁴-10⁻⁶ M⁻¹, less than about 10⁻⁵ to10⁻⁹ M⁻¹, or less than about 10⁻⁷-10⁻⁹ M⁻¹.

“Fluorescent label,” “fluorescent moiety,” and “fluorophore” refer to amolecule that may be detected via its inherent fluorescent properties.Examples of suitable fluorescent labels include, but are not limited to,fluorescein, rhodamine, tetramethylrhodamine, eosin, erythrosin,coumarin, methyl-coumarins, pyrene, Malachite Green, stilbene, LuciferYellow, Cascade BlueJ, Texas Red, IAEDANS, EDANS, BODIPY FL, LC Red 640,phycoerythrin, LC Red 705, Oregon green, Alexa-Fluor dyes (Alexa Fluor350, Alexa Fluor 430, Alexa Fluor 488, Alexa Fluor 546, Alexa Fluor 568,Alexa Fluor 594, Alexa Fluor 633, Alexa Fluor 660, Alexa Fluor 680),Cascade Blue, Cascade Yellow and R-phycoerythrin (PE), FITC, Rhodamine,Texas Red (Pierce, Rockford, Ill.), Cy5, Cy5.5, Cy7 (Amersham LifeScience, Pittsburgh, Pa.) and tandem conjugates, such as but not limitedto, Cy5PE, Cy5.5PE, Cy7PE, Cy5.5APC, Cy7APC. In some embodiments,suitable fluorescent labels also include, but are not limited to, greenfluorescent protein (GFP; Chalfie, et al., 1994, Science263(5148):802-805), EGFP (Clontech Laboratories, Inc., Palo Alto,Calif.), blue fluorescent protein (BFP; Quantum Biotechnologies, Inc.Montreal, Canada; Heim et al, 1996, Curr. Biol. 6:178-182; Stauber,1998, Biotechniques 24(3):462-471;), enhanced yellow fluorescent protein(EYFP; Clontech Laboratories, Inc., Palo Alto, Calif.), and renilla (WO92/15673; WO 95/07463; WO 98/14605; WO 98/26277; WO 99/49019; U.S. Pat.Nos. 5,292,658, 5,418,155, 5,683,888, 5,741,668, 5,777,079, 5,804,387,5,874,304, 5,876,995, and 5,925,558). Further examples of fluorescentlabels are found in Haugland, Handbook of Fluorescent Probes andResearch, 9^(th) Edition, Molecule Probes, Inc. Eugene, Oreg. (ISBN0-9710636-0-5).

In some embodiments, a label can be a microparticle. By “microparticle”,“microsphere”, “microbead”, “bead” and grammatical equivalents hereinare meant a small discrete synthetic particle. As known in the art, thecomposition of beads can vary depending on the type of assay in whichthey are used and, therefore, selecting a microbead composition iswithin the abilities of the practitioner. Suitable bead compositionsinclude those used in peptide, nucleic acid and organic synthesis,including, but not limited to, plastics, ceramics, glass, polystyrene,methylstyrene, acrylic polymers, paramagnetic materials (U.S. Pat. Nos.4,358,388, 4,654,267, 4,774,265, 5,320,944, 5,356,713), thoria sol,carbon graphite, titanium dioxide, latex or cross-linked dextrans suchas Sepharose, agarose, cellulose, carboxymethyl cellulose, hydroxyethylcellulose, proteinaceous polymer, nylon, globulin, DNA, cross-linkedmicelles and Teflon may all be used (see, e.g., Microsphere DetectionGuide from Bangs Laboratories, Fishers, Ind.), Beads are alsocommercially available from, for example, Bio-Rad Laboratories(Richmond, Calif.), LKB (Sweden), Pharmacia (Piscataway, N.J.), IBF(France), Dynal Inc. (Great Neck, N.Y.). In some embodiments, beads maycontain a cross-linking agent, such as, but not limited to divinylbenzene, ethylene glycol dimethacrylate, trimethylol propanetrimethacrylate, N,N′methylene-bis-acrylamide, adipic acid, sebacicacid, succinic acid, citric acid, 1,2,3,4-butanetetracarboxylic acid, or1,10 decanedicarboxylic acid or other functionally equivalent agentsknown in the art. In various exemplary embodiments, beads can bespherical, non-spherical, egg-shaped, irregularly shaped, and the like.The average diameter of a microparticle can be selected at thediscretion of the practitioner. However, generally the average diameterof microparticle can range from nanometers (e.g. about 100 nm) tomillimeters (e.g. about 1 mm) with beads from about 0.2 μm to about 200μm being preferred, and from about 0.5 to about 10 μm being particularlypreferred, although in some embodiments smaller or larger beads may beused, as described below.

In some embodiments a microparticle can be porous, thus increasing thesurface area available for attachment to another molecule, moiety, orcompound (e.g., a primer). Thus, microparticles may have additionalsurface functional groups to facilitate attachment and/or bonding. Thesegroups may include carboxylates, esters, alcohols, carbamides,aldehydes, amines, sulfur oxides, nitrogen oxides, or halides. Methodsof attaching another molecule or moiety to a bead are known in the art(see, e.g., U.S. Pat. Nos. 6,268,222, 6,649,414). In some embodiments, amicroparticle can further comprise a label.

The compositions and reagents described herein can be packaged intokits. In some embodiments, a kit comprises a reagent for making aninverse emulsion comprising one or more aqueous compartments. In someembodiments, the aqueous compartments can be used in conjunction withone or more reagents from commercially available kits, including, butnot limited to, those available from Applied Biosystems (i.e., Big Dye®Terminator Cycle Sequencing Kit), Epicentre (i.e., SequiTherm™ CycleSequencing Kit), Amersham (i.e., DYEnamic Direct Dye-Primer CycleSequencing Kits), Boehringer Mannheim (i.e., CycleReader™ DNA SequencingKit), Bionexus Inc. (i.e., AccuPower DNA Sequencing Kit), and USB cyclesequencing kits (i.e., Thermo Sequenase™ Cycle Sequencing Kit).

In some embodiments, a kit can comprise a primer suitable for multiplexor clonal amplification. In some embodiments, a primer can be attachedto a surface, such as, a microparticle and/or a slide and the like. Insome embodiments each primer can comprise a target specific sequenceand/or a universal sequence. In some embodiments, the microparticles canfurther comprise various labels, including but not limited to,fluorescent and/or magnetic labels. In some embodiments, a kit cancomprise a library of primers or primer pairs. In some embodiments, akit can comprise one or more reaction compartments comprising reagentssuitable for performing a reaction selected at the discretion of apractitioner. For example, in some embodiments, a kit can comprise oneor more reaction compartments comprising one more sequencing reagents.

The various components included in the kit are typically contained inseparate containers, however, in some embodiments, one or more of thecomponents can be present in the same container. Additionally, kits cancomprise any combination of the compositions and reagents describedherein. In some embodiments, kits can comprise additional reagents thatmay be necessary or optional for performing the disclosed methods. Suchreagents include, but are not limited to, buffers, molecular sizestandards, control polynucleotides, and the like.

In this application, the use of the singular includes the plural unlessspecifically stated otherwise. The section headings used herein are fororganizational purposes only and are not to be construed as limiting thesubject matter described in any way. While the present teachings aredescribed in conjunction with various embodiments, it is not intendedthat the present teachings be limited to such embodiments. On thecontrary, the present teachings encompass various alternatives,modifications, and equivalents, as will be appreciated by those of skillin the art.

All literature and similar materials cited in this application,including but not limited to, patents, patent applications, articles,books, and treatises, regardless of the format of such literature andsimilar materials, are expressly incorporated by reference in theirentirety for any purpose. In the event that one or more of theincorporated literature and similar materials differs from orcontradicts this application, including but not limited to definedterms, term usage, described techniques, or the like, this applicationcontrols.

1. A method of analyzing a plurality of polynucleotides comprising: a)amplifying a plurality of polynucleotides under conditions suitable toproduce a plurality of multiplex amplicons; b) clonally amplifying saidmultiplex amplicons to produce a plurality of clonal amplicons; and c)analyzing said plurality of clonal amplicons.
 2. The method according toclaim 1, wherein said plurality of polynucleotides is at least about 100polynucleotides.
 3. The method according to claim 1, wherein saidplurality of polynucleotides is at least about 1000 polynucleotides. 4.The method according to claim 1, wherein said plurality ofpolynucleotides is at least about 10,000 polynucleotides.
 5. The methodaccording to claim 1, wherein said plurality of polynucleotides is atleast about 100,000 polynucleotides.
 6. The method according to claim 1,wherein said plurality of polynucleotides is at least about 1,000,000polynucleotides.
 7. (canceled)
 8. (canceled)
 9. The method according toclaim 1, wherein said multiplex amplicons are clonally amplified inhydrophilic compartments of an inverse emulsion.
 10. The methodaccording to claim 9, wherein said hydrophilic compartments are disposedupon a surface.
 11. The method according to claim 10, wherein saidsurface comprises primers suitable for clonally amplifying saidmultiplex amplicons.
 12. The method according to claim 11, wherein saidprimers are hybridized to said multiplex amplicons.
 13. The methodaccording to claim 12, wherein said clonal amplicons are attached tosaid surface.
 14. The method according to claim 1, wherein saidconditions suitable for producing said plurality of multiplex ampliconscomprise multiple rounds of a thermocycling reaction comprising forwardand reverse amplification primer pairs, a thermostable polymerase, anddeoxynucleotide triphosphate suitable for DNA synthesis.
 15. The methodaccording to claim 14, wherein said multiple rounds of a thermocyclingreaction terminates before said reaction reaches a plateau.
 16. Themethod according to claim 14, wherein said forward primers comprises aforward universal sequence and said reverse primers comprise a reverseuniversal sequence.
 17. (canceled)
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 22. The method according to claim 1, whereinsaid analyzing comprises sequencing said plurality of clonal amplicons.23. The method according to claim 22, wherein said sequencing comprisingsequencing in parallel.
 24. The method according to claim 22, whereinsaid sequencing is massively parallel signature sequence.
 25. (canceled)26. (canceled)
 27. (canceled)
 28. A method of amplifying a plurality ofpolynucleotides comprising: hybridizing polynucleotides isolated inhydrophilic compartments of an inverse emulsion to primers, wherein saidprimers are attached to a surface and said compartments are disposedupon said surface, and wherein said polynucleotides and said primers arehybridized in the presence of a polymerase and nucleotide triphosphatessuitable for nucleic acid synthesis and under conditions suitable forsaid polymerase to extend said primers, whereby said polynucleotides areamplified.
 29. (canceled)
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 32. (canceled)33. (canceled)
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 35. A method of analyzing a plurality ofpolynucleotides comprising: a) clonally amplifying a plurality ofpolynucleotides in hydrophilic compartments of an inverse emulsion inthe presence of primers, a polymerase, and nucleotide triphosphatessuitable for nucleic acid synthesis, wherein said primer is attached toa surface and said compartment is disposed upon said surface, and underconditions suitable to produce a plurality of clonal amplicons attachedto said surface; and b) analyzing said plurality of clonal amplicons.36. (canceled)
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 39. (canceled) 40.(canceled)
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 48. (canceled) 49.(canceled)
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 51. A composition comprising an inverseemulsion and an oligonucleotide attached to a surface, wherein saidinverse emulsion comprises at least one hydrophilic compartment that isdisposed upon a said surface and wherein said oligonucleotide is incontact with said hydrophilic compartment.
 52. (canceled)